rs2306327

Variant names:

• chr10-73814020-A-T
• rs2306327
• NM_001367534.1:c.*498T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367534.1(CAMK2G):​c.*498T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,496 control chromosomes in the GnomAD database, including 1,356 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.13 (1356 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: CAMK2G NM_001367534.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 11 publications found

Genes affected

CAMK2G (HGNC:1463): (calcium/calmodulin dependent protein kinase II gamma) The product of this gene is one of the four subunits of an enzyme which belongs to the serine/threonine protein kinase family, and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a gamma chain. Many alternatively spliced transcripts encoding different isoforms have been described but the full-length nature of all the variants has not been determined.[provided by RefSeq, Mar 2011]

CAMK2G-AS1 (HGNC:56057): (CAMK2G antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367534.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK2G	NM_001367534.1	MANE Select	c.*498T>A		3_prime_UTR	Exon 23 of 23	NP_001354463.1	H0Y6G2
	CAMK2G	NM_001367544.1		c.*498T>A		3_prime_UTR	Exon 22 of 22	NP_001354473.1
	CAMK2G	NM_001367548.1		c.*498T>A		3_prime_UTR	Exon 23 of 23	NP_001354477.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK2G	ENST00000423381.6	TSL:5 MANE Select	c.*498T>A		3_prime_UTR	Exon 23 of 23	ENSP00000410298.3	H0Y6G2
	CAMK2G	ENST00000322635.7	TSL:1	c.*498T>A		3_prime_UTR	Exon 21 of 21	ENSP00000315599.3	Q13555-5
	CAMK2G	ENST00000864109.1		c.*498T>A		3_prime_UTR	Exon 22 of 22	ENSP00000534168.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19569 AN: 152070 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.149 AC: 46 AN: 308 Hom.: 0 Cov.: 0 AF XY: 0.153 AC XY: 30 AN XY: 196

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.151 AC: 45 AN: 298

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.129 AC: 19617 AN: 152188 Hom.: 1356 Cov.: 32 AF XY: 0.129 AC XY: 9563 AN XY: 74410

African (AFR) AF: 0.117 AC: 4865 AN: 41524

American (AMR) AF: 0.102 AC: 1557 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.125 AC: 647 AN: 5166

South Asian (SAS) AF: 0.193 AC: 933 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10594

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9007 AN: 68000

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.135 Hom.: 196

Bravo AF: 0.127

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2306327; hg19: chr10-75573778;